2YEV

Structure of caa3-type cytochrome oxidase

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	COX3	e2yevA4	A: alpha bundles	X: Cytochrome c oxidase subunit III-like (From Topology)	H: Cytochrome c oxidase subunit III-like (From Topology)	T: Cytochrome c oxidase subunit III-like	F: COX3	ECOD (1.6)
A	COX1	e2yevA2	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1	ECOD (1.6)
D	COX3	e2yevD1	A: alpha bundles	X: Cytochrome c oxidase subunit III-like (From Topology)	H: Cytochrome c oxidase subunit III-like (From Topology)	T: Cytochrome c oxidase subunit III-like	F: COX3	ECOD (1.6)
D	COX1	e2yevD2	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1	ECOD (1.6)
B	COX2	e2yevB4	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
B	Cytochrom_C	e2yevB6	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrom_C	ECOD (1.6)
B	COX2_TM_1	e2yevB5	A: extended segments	X: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	H: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	T: Cytochrome c oxidase subunit II-like, transmembrane region	F: COX2_TM_1	ECOD (1.6)
E	COX2	e2yevE10	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
E	Cytochrom_C	e2yevE12	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrom_C	ECOD (1.6)
E	COX2_TM_1	e2yevE11	A: extended segments	X: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	H: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	T: Cytochrome c oxidase subunit II-like, transmembrane region	F: COX2_TM_1	ECOD (1.6)
C	Caa3-IV	e2yevC1	A: extended segments	X: CAA3-type cytochrome c oxidase subunit IV (From Topology)	H: CAA3-type cytochrome c oxidase subunit IV (From Topology)	T: CAA3-type cytochrome c oxidase subunit IV	F: Caa3-IV	ECOD (1.6)
F	Caa3-IV	e2yevF1	A: extended segments	X: CAA3-type cytochrome c oxidase subunit IV (From Topology)	H: CAA3-type cytochrome c oxidase subunit IV (From Topology)	T: CAA3-type cytochrome c oxidase subunit IV	F: Caa3-IV	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
A	1.10.287.70	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
A	1.20.120.80	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c oxidase, subunit III, four-helix bundle	CATH (4.3.0)
D	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
D	1.10.287.70	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D	1.20.120.80	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c oxidase, subunit III, four-helix bundle	CATH (4.3.0)
B	1.10.287.90	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
E	1.10.287.90	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
E	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
C	6.10.280.110	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
F	6.10.280.110	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF00510	Cytochrome c oxidase subunit III (COX3)	Cytochrome c oxidase subunit III	-	Family
A, D	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
B, E	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain	-	Domain
B, E	PF02790	Cytochrome C oxidase subunit II, transmembrane domain (COX2_TM)	Cytochrome C oxidase subunit II, transmembrane domain	-	Family
B, E	PF00034	Cytochrome c (Cytochrom_C)	Cytochrome c	The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.	Domain
C, F	PF20814	CAA3-type cytochrome c oxidase subunit IV (CAA3_Cox_suIV)	CAA3-type cytochrome c oxidase subunit IV	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	CYTOCHROME C OXIDASE POLYPEPTIDE I+III	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds cellular metabolic process metabolic process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	membrane respirasome cellular anatomical entity cell periphery plasma membrane
B, E	CYTOCHROME C OXIDASE SUBUNIT 2	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding small molecule binding	-	membrane respirasome cellular anatomical entity cell periphery plasma membrane
C, F	CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV	-	-	membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A, D	IPR000883	Cytochrome c oxidase subunit I	Family
A, D	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A, D	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
A, D	IPR035973	Cytochrome c oxidase subunit III-like superfamily	Homologous Superfamily
A, D	IPR000298	Cytochrome c oxidase subunit III-like	Domain
A, D	IPR014241	Cytochrome c oxidase, subunit I bacterial type	Family
A, D	IPR013833	Cytochrome c oxidase, subunit III, 4-helical bundle	Homologous Superfamily
B, E	IPR011759	Cytochrome C oxidase subunit II, transmembrane domain	Domain
B, E	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
B, E	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B, E	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
B, E	IPR034236	Caa3-type Cytochrome c oxidase subunit II, cupredoxin domain	Domain
B, E	IPR009056	Cytochrome c-like domain	Domain
B, E	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B, E	IPR008972	Cupredoxin	Homologous Superfamily
B, E	IPR001505	Copper centre Cu(A)	Binding Site
B, E	IPR014222	Cytochrome c oxidase, subunit II	Domain
C, F	IPR038405	Cytochrome oxidase Caa3-type, subunit IV superfamily	Homologous Superfamily
C, F	IPR033793	Cytochrome oxidase Caa3-type, subunit IV	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex IV (cytochrome c oxidase)	Cytochrome c oxidases

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)	Cytochrome C Oxidase, caa₃

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, F	FME	Parent Component: MET RESID: AA0021 , AA0566 PSI-MOD : N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891